業績一覧|理化学研究所 生命機能科学研究センター(BDR)

業績一覧タンパク質機能・構造研究チーム

  1. Tanaka, M., Ishige, A., Yaguchi, M., Matsumoto, T., Shirouzu, M., Yokoyama, S., Ishikawa, F., Kitabayashi, I., Takemori, T. and Harada, M. "Development of a simple new flow cytometric antibody-dependent cellular cytotoxicity (ADCC) assay with excellent sensitivity”, Journal of Immunol Methods, (2018), doi: 10.1016/j.jim.2018.10.014
  2. Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M. and Sekine, SI., "Structural basis of the nucleosome transition during RNA polymerase II passage", Science, 362(6414), 595-598 (2018)
  3. Shigematsu, H., Imasaki, T., Doki, C., Sumi, T., Aoki, M., Uchikubo-Kamo, T., Sakamoto, A., Tokuraku, K., Shirouzu, M. and Nitta, R. "Structural insight into microtubule stabilization and kinesin inhibition by Tau-family MAPs.", J. Cell Biol., 217(12), 4155-4163 (2018)
  4. Shima, T., Morikawa, M., Kaneshiro, J., Kambara. T., Kamimura, S., Yagi, T., Iwamoto, H., Uemura, S., Shigematsu, H., Shirouzu, M., Ichimura, T., Watanabe, T. M., Nitta, R., Okada, Y. and Hirokawa, N. "Kinesin-binding–triggered conformation switching of microtubules contributes to polarized transport", J. Cell Biol., 217(12), 4164-4183 (2018)
  5. Ohbayashi, N., Murayama, K., Kato-Murayama, M., Kukimoto-Niino, M., Uejima, T., Matsuda, T., Ohsawa, N., Yokoyama, S., Nojima ,H. and Shirouzu, M. "Structural Basis for the Inhibition of Cyclin G-Associated Kinase by Gefitinib", ChemistryOpen, 7(9), 721-727 (2018)
  6. Ueda, H., Matsunaga, H., Matsushita, Y., Maeda, S., Iwamoto, R., Yokoyama, S. and Shirouzu M. "Ecto-F0/F1 ATPase as a novel candidate of prothymosin α receptor", Expert Opinion on Biological Therapy, 18(1), 89-94 (2018)
  7. Sakurai, T., Uruno, T., Sugiura, Y., Tatsuguchi, T., Yamamura, K., Ushijima, M., Hattori, Y., Kukimoto-Niino, M., Mishima-Tsumagari, C., Watanabe, M., Suematsu, M., Fukui, Y., "Cholesterol sulfate is a DOCK2 inhibitor that mediates tissue-specific immune evasion in the eye", Sci. Signal., 11(541), eaao4874 (2018)
  8. Kasuya, G., Nakane, T., Yokoyama, T., Jia, Y., Inoue, M., Watanabe, K., Nakamura, R., Nishizawa, T., Kusakizako, T., Tsutsumi, A., Yanagisawa, H., Dohmae, N., Hattori, M., Ichijo, H., Yan, Z., Kikkawa, M., Shirouzu, M., Ishitani, R. and Nureki, O. "Cryo-EM structures of the human volume-regulated anion channel LRRC8" Nat. Struct. Mol. Biol., 25 (9), 797-804 (2018)
  9. Katsura, K., Tomabechi, Y., Matsuda, T., Yonemochi, M., Mikunia, J., Ohsawa, N., Terada, T., Yokoyama, S., Kukimoto-Niino, M., Takemoto, C. and Shirouzu, M. "Phosphorylated and non-phosphorylated HCK kinase domains produced by cell-free protein expression", Protein Expr. Purif., 150 92-99 (2018).
  10. Inouye, S., Tomabechi, Y., Hosoya, T., Sekine, SI. and Shirouzu, M. "Slow luminescence kinetics of semi-synthetic aequorin: Expression, purification and structure determination of cf3-aequorin", J.Biochem., 164(3), 247-255 (2018).
  11. Yamagata, A., Miyazaki, Y., Yokoi, N., Shigematsu, H., Sato, Y., Goto-Ito, S., Maeda, A., Goto, T., Sanbo, M., Hirabayashi, M., Shirouzu, M., Fukata, Y., Fukata, M. and Fukai, S. "Structural basis of epilepsy-related ligand-receptor complex LGI1-ADAM22", Nat Commun., 9(1), 1546, (2018).
  12. Tamogami, J., Kikukawa, T., Ohkawa, K., Ohsawa, N., Nara, T., Demura, M., Miyauchi, S., Kimura-Someya, T., Shirouzu, M., Yokoyama, S., Shimono, K. and Kamo, N. "Interhelical interactions between D92 and C218 in the cytoplasmic domain regulate proton uptake upon N-decay in the proton transport of Acetabularia rhodopsin II", J Photochem Photobiol B. 183, 35-45, (2018).
  13. Nishio, K., Belle, R., Katoh, T., Kawamura, A., Sengoku, T., Hanada, K., Ohsawa, N., Shirouzu, M., Yokoyama, S. and Suga, H. "Thioether Macrocyclic Peptides Selected against TET1 Compact Catalytic Domain Inhibit TET1 Catalytic Activity", Chembiochem. 19(9), 979-985, (2018).
  14. Sumi, T., Imasaki, T., Aoki, M., Sakai, N., Nitta, E., Shirouzu, M. and Nitta R. "Structural Insights into the Altering Function of CRMP2 by Phosphorylation", Cell Struct Funct., 43(1),15-23(2018).
  15. Matsuda, T., Ito, T., Takemoto, C., Katsura, K., Ikeda, M., Wakiyama, M., Kukimoto-Niino, M., Yokoyama, S., Kurosawa, Y. and Shirouzu, M. "Cell-free synthesis of functional antibody fragments to provide a structural basis for antibody-antigen interaction", PLoS One,13(2) e0193158(2018).
  16. Hori, T., Okuno, T., Hirata, K., Yamashita, K., Kawano, Y., Yamamoto, M., Hato, M., Nakamura, M., Shimizu, T., Yokomizo, T., Miyano, M. and Yokoyama, S. "Na+-mimicking ligands stabilize the inactive state of leukotriene B4 receptor BLT1", Nat Chem Biol., 14, 262-269 (2018).
  17. Koda, Y., Kikuzato, K., Mikuni, J., Tanaka, A., Yuki, H., Honma, T., Tomabechi, Y., Kukimoto-Niino, M., Shirouzu, M., Shirai, F. and Koyama, H. "Identification of pyrrolo[2,3-d]pyrimidines as potent HCK and FLT3-ITD dual inhibitors", Bioorg. Med. Chem. Lett., 27 (22), 4994-4998 (2017).
  18. Hasegawa, K., Someya, Y., Shigematsu, H., Kimura-Someya, T., Nuemket, N. and Kumasaka, T. "Crystallization and X-ray analysis of 23 nm virus-like particles from Norovirus Chiba strain", Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 73 (10), 568-573 (2017).
  19. Shoji, S., Hanada, K., Ohsawa, N. and Shirouzu, M. "Central catalytic domain of BRAP (RNF52) recognizes the types of ubiquitin chains and utilizes oligo-ubiquitin for ubiquitylation", Biochem. J., 474 (18), 3207-3226 (2017).
  20. Niwa, S., Nakamura, F., Tomabechi, Y., Aoki, M., Shigematsu, H., Matsumoto, T., Yamagata, A., Fukai, S., Hirokawa, N., Goshima, Y., Shirouzu, M. and Nitta, R. "Structural basis for CRMP2-induced axonal microtubule formation", Sci Rep, 7 (1), 10681 (2017).
  21. Chase, A. R., Laudermilch, E., Wang, J., Shigematsu, H., Yokoyama, T. and Schlieker, C. "Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1", Mol. Biol. Cell, 28 (21), 2765-2772 (2017).
  22. Iwaoka, R., Nagata, T., Tsuda, K., Imai, T., Okano, H., Kobayashi, N. and Katahira, M. "Backbone and side chain assignments of the second RNA-binding domain of Musashi-1 in its free form and in complex with 5-mer RNA", Biomol NMR Assign, 11 (2), 265-268 (2017).
  23. Ehara, H., Yokoyama, T., Shigematsu, H., Yokoyama, S., Shirouzu, M. and Sekine, SI. "Structure of the complete elongation complex of RNA polymerase II with basal factors", Science, 357 (6354), 921-924 (2017).
  24. Iwaoka, R., Nagata, T., Tsuda, K., Imai, T., Okano, H., Kobayashi, N. and Katahira, M. "Structural Insight into the Recognition of r(UAG) by Musashi-1 RBD2, and Construction of a Model of Musashi-1 RBD1-2 Bound to the Minimum Target RNA", Molecules, 22 (7), 1207 (2017).
  25. Shimizu, H., Tosaki, A., Ohsawa, N., Ishizuka-Katsura, Y., Shoji, S., Miyazaki, H., Oyama, F., Terada, T., Shirouzu, M., Sekine, SI., Nukina, N. and Yokoyama, S. "Parallel homodimer structures of the extracellular domains of the voltage-gated sodium channel β4 subunit explain its role in cell-cell adhesion", J. Biol. Chem., 292 (32), 13428-13440 (2017).
  26. Hosaka, T., Okazaki, M., Kimura-Someya, T., Ishizuka-Katsura, Y., Ito, K., Yokoyama, S., Dodo, K., Sodeoka, M. and Shirouzu, M. "Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1", Protein Sci., 26 (9), 1749-1758 (2017).
  27. López-Alonso, J. P., Kaminishi, T., Kikuchi, T., Hirata, Y., Iturrioz, I., Dhimole, N., Schedlbauer, A., Hase, Y., Goto, S., Kurita, D., Muto, A., Zhou, S., Naoe, C., Mills, D. J., Gil-Carton, D., Takemoto, C., Himeno, H., Fucini, P. and Connell, S. R. "RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket", Nucleic Acids Res., 45 (11), 6945-6959 (2017).
  28. Yuki, H., Kikuzato, K., Koda, Y., Mikuni, J., Tomabechi, Y., Kukimoto-Niino, M., Tanaka, A., Shirai, F., Shirouzu, M., Koyama, H. and Honma, T. "Activity cliff for 7-substituted pyrrolo-pyrimidine inhibitors of HCK explained in terms of predicted basicity of the amine nitrogen", Bioorg. Med. Chem., 25 (16), 4259-4264 (2017).
  29. Katsura, K., Matsuda, T., Tomabechi, Y., Yonemochi, M., Hanada, K., Ohsawa, N., Sakamoto, K., Takemoto, C. and Shirouzu, M. "A reproducible and scalable procedure for preparing bacterial extracts for cell-free protein synthesis", J. Biochem., 162 (5), 357-369 (2017).
  30. Iwakura, N., Yokoyama, T., Quaglia, F., Mitsuoka, K., Mio, K., Shigematsu, H., Shirouzu, M., Kaji, A. and Kaji, H. "Chemical and structural characterization of a model Post-Termination Complex (PoTC) for the ribosome recycling reaction: Evidence for the release of the mRNA by RRF and EF-G", PLoS ONE., 12(5), e0177972 (2017).
  31. Nagano-Shoji, M., Hamamoto, Y., Mizuno, Y., Yamada, A., Kikuchi, M., Shirouzu, M., Umehara, T., Yoshida, M., Nishiyama, M. and Kosono, S. "Characterization of lysine acetylation of a phosphoenolpyruvate carboxylase involved in glutamate overproduction in Corynebacterium glutamicum", Mol. Microbiol., 104 (4), 677-689 (2017).
  32. Tajiri, H., Uruno, T., Shirai, T., Takaya, D., Matsunaga, S., Setoyama, D., Watanabe, M., Kukimoto-Niino, M., Oisaki, K., Ushijima, M., Sanematsu, F., Honma, T., Terada, T., Oki, E., Shirasawa, S., Maehara, Y., Kang, D., Côté, JF., Yokoyama, S., Kanai, M. and Fukui, Y. "Targeting Ras-Driven Cancer Cell Survival and Invasion through Selective Inhibition of DOCK1", Cell Rep, 19 (5), 969-980 (2017).
  33. Tamogami, J., Kikukawa, T., Nara, T., Demura, M., Kimura-Someya, T., Shirouzu, M., Yokoyama, S., Miyauchi, S., Shimono, K. and Kamo, N. "Existence of two O-like intermediates in the photocycle of Acetabularia rhodopsin II, a light-driven proton pump from a marine alga", Biophys Physicobiol, 14, 49-55 (2017).
  34. Nango, E., Royant, A., Kubo, M., Nakane, T., Wickstrand, C., Kimura, T., Tanaka, T., Tono, K., Song, C., Tanaka, R., Arima, T., Yamashita, A., Kobayashi, J., Hosaka, T., Mizohata, E., Nogly, P., Sugahara, M., Nam, D., Nomura, T., Shimamura, T., Im, D., Fujiwara, T., Yamanaka, Y., Jeon, B., Nishizawa, T., Oda, K., Fukuda, M., Andersson, R., Båth, P., Dods, R., Davidsson, J., Matsuoka, S., Kawatake, S., Murata, M., Nureki, O., Owada, S., Kameshima, T., Hatsui, T., Joti, Y., Schertler, G., Yabashi, M., Bondar, AN., Standfuss, J., Neutze, R. and Iwata, S. “A three-dimensional movie of structural changes in bacteriorhodopsin”, Science, 354 (6319), 1552-1557 (2016).
  35. Kuwasako, K., Nameki, N., Tsuda, K., Takahashi, M., Sato, A., Tochio, N., Inoue, M., Terada, T., Kigawa, T., Kobayashi, N., Shirouzu, M., Ito, T., Sakamoto, T., Wakamatsu, K., Güntert, P., Takahashi, S., Yokoyama, S. and Muto, Y. "Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment", Protein Sci., 26 (2), 280-291 (2016).
  36. Nakane, T., Hanashima, S., Suzuki, M., Saiki, H., Hayashi, T., Kakinouchi, K., Sugiyama, S., Kawatake, S., Matsuoka, S., Matsumori, N., Nango, E., Kobayashi, J., Shimamura, T., Kimura, K., Mori, C., Kunishima, N., Sugahara, M., Takakyu, Y., Inoue, S., Masuda, T., Hosaka, T., Tono, K., Joti, Y., Kameshima, T., Hatsui, T., Yabashi, M., Inoue, T., Nureki, O., Iwata, S., Murata, M. and Mizohata, E. "Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent", Proc. Natl. Acad. Sci. U.S.A., 113 (46) 13039-13044 (2016).
  37. Muramatsu, T., Takemoto, C., Kim, YT., Wang, H., Nishii, W., Terada, T., Shirouzu, M. and Yokoyama, S. "SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity", Proc. Natl. Acad. Sci. U.S.A., 113 (46), 12997-13002 (2016).
  38. Konomura, N., Arai, N., Shinohara, T., Kobayashi, J., Iwasaki, W., Ikawa, S., Kusano, K. and Shibata, T. "Rad51 and RecA juxtapose dsDNA ends ready for DNA ligase-catalyzed end-joining under recombinase-suppressive conditions", Nucleic Acids Res., 45 (1), 337-352 (2016).
  39. Suzuki, K., Mizutani, K., Maruyama, S., Shimono, K., Imai, FL., Muneyuki, E., Kakinuma, Y., Ishizuka-Katsura, Y., Shirouzu, M., Yokoyama, S., Yamato, I. and Murata, T. "Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor", Nat Commun., 7, 13235 (2016).
  40. Wang, D., Nitta, R., Morikawa, M., Yajima, H., Inoue, S., Shigematsu, H., Kikkawa, M. and Hirokawa, N. "Motility and microtubule depolymerization mechanisms of the Kinesin-8 motor, KIF19A", ELife, 5, e18101 (2016).
  41. Shinoda, T., Shinya, N., Ito, K., Ohsawa, N., Terada, T., Hirata, K., Kawano, Y., Yamamoto, M., Kimura-Someya, T., Yokoyama, S. and Shirouzu, M. "Structural basis for disruption of claudin assembly in tight junctions by an enterotoxin", Sci Rep, 6, 33632 (2016).
  42. Terasawa, K., Tomabechi, Y., Ikeda, M., Ehara, H., Kukimoto-Niino, M., Wakiyama, M., Podyma-Inoue, K. A., Rajapakshe, A. R., Watabe, T., Shirouzu, M. and Hara-Yokoyama, M. "Lysosome-associated membrane proteins-1 and -2 (LAMP-1 and LAMP-2) assemble via distinct modes", Biochem. Biophys. Res. Commun., 479 (3), 489-495 (2016).
  43. Sotokawauchi, A., Kato-Murayama, M., Murayama, K., Hosaka, T., Maeda, I., Onjo, M., Ohsawa, N., Kato, DI., Arima, K. and Shirouzu, M. "Structural Basis of Cucumisin Protease Activity Regulation by Its Propeptide", J. Biochem., 161 (1), 45-53 (2016).
  44. Masuda, M., Uno, Y., Ohbayashi, N., Ohata, H., Mimata, A., Kukimoto-Niino, M., Moriyama, H., Kashimoto, S., Inoue, T., Goto, N., Okamoto, K., Shirouzu, M., Sawa, M. and Yamada, T. "TNIK inhibition abrogates colorectal cancer stemness", Nat Commun., 7, 12586 (2016).
  45. Shinoda, T., Shinya, N., Ito, K., Ishizuka-Katsura, Y., Ohsawa, N., Terada, T., Hirata, K., Kawano, Y., Yamamoto, M., Tomita, T., Ishibashi, Y., Hirabayashi, Y., Kimura-Someya, T., Shirouzu, M. and Yokoyama, S. "Cell-free methods to produce structurally intact mammalian membrane proteins", Sci Rep, 6, 30442 (2016).
  46. Yamagishi, M., Shigematsu, H., Yokoyama, T., Kikkawa, M., Sugawa, M., Aoki, M., Shirouzu, M., Yajima, J. and Nitta, R. "Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility", Structure, 24 (8), 1322-1334 (2016).
  47. Hosaka, T., Yoshizawa, S., Nakajima, Y., Ohsawa, N., Hato, M., DeLong, E. F., Kogure, K., Yokoyama, S., Kimura-Someya, T., Iwasaki, W. and Shirouzu, M. "Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3", J. Biol. Chem., 291 (34), 17488-17495 (2016).
  48. Verba, K. A., Wang, R. Y., Arakawa, A., Liu, Y., Shirouzu, M., Yokoyama, S. and Agard, D. A. "Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase", Science, 352 (6293), 1542-1547 (2016).
  49. Yip, W. S., Shigematsu, H., Taylor, D. W. and Baserga, S. J. "Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs", Nucleic Acids Res., 44 (18), 8976-8989 (2016).
  50. Shimizu, H., Miyazaki, H., Ohsawa, N., Shoji, S., Ishizuka-Katsura, Y., Tosaki, A., Oyama, F., Terada, T., Sakamoto, K., Shirouzu, M., Sekine, S., Nukina, N. and Yokoyama, S. "Structure-based site-directed photo-crosslinking analyses of multimeric cell-adhesive interactions of voltage-gated sodium channel β subunits", Sci Rep, 6, 26618 (2016).
  51. Suenaga, T., Watanabe-Matsui, M., Uejima, T., Shima, H., Matsui, T., Ikeda-Saito, M., Shirouzu, M., Igarashi, K. and Murayama, K. "Charge-state-distribution analysis of Bach2 intrinsically disordered heme binding region", J. Biochem., 160 (5), 291-298 (2016).
  52. Fabbretti, A., Schedlbauer, A., Brandi, L., Kaminishi, T., Giuliodori, AM., Garofalo, R., Ochoa-Lizarralde, B., Takemoto, C., Yokoyama, S., Connell, SR., Gualerzi, CO. and Fucini, P. "Inhibition of translation initiation complex formation by GE81112 unravels a 16S rRNA structural switch involved in P-site decoding", Proc. Natl. Acad. Sci. U.S.A., 113 (16), E2286-2295 (2016).
  53. Rahman, S., Yamato, I., Saijo, S., Mizutani, K., Takamuku, Y., Ishizuka-Katsura, Y., Ohsawa, N., Terada, T., Shirouzu, M., Yokoyama, S., and Murata, T. "Binding interactions of the peripheral stalk subunit isoforms from human V-ATPase", Biosci. Biotechnol. Biochem., 80 (5), 878-890 (2016).
  54. Jeong, H., Kim, JS., Song, S., Shigematsu, H., Yokoyama, T., Hyun, J., and Ha, NC. "Pseudoatomic Structure of the Tripartite Multidrug Efflux Pump AcrAB-TolC Reveals the Intermeshing Cogwheel-like Interaction between AcrA and TolC", Structure, 24 (2), 272–276 (2016).
  55. Jensen, K. H., Brandt, S. S., Shigematsu, H., and Sigworth, F. J. "Statistical modeling and removal of lipid membrane projections for cryo-EM structure determination of reconstituted membrane proteins", J. Struct. Biol., 194 (1), 49–60 (2016).
  56. Tomabechi, Y., Hosoya, T., Ehara, H., Sekine, S., Shirouzu, M., and Inouye, S. "Crystal structure of nanoKAZ: The mutated 19 kDa component of Oplophorus luciferase catalyzing the bioluminescent reaction with coelenterazine", Biochem. Biophys. Res. Commun., 470 (1), 88–93 (2016).
  57. Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., and Yokoyama, S. "Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation", Sci Rep, 5, 17204 (2015).
  58. Nagano, S., Seki, E., Lin, TY., Shirouzu, M., Yokoyama, S., and Heddle, J. G. "Investigating the Roles of the C-Terminal Domain of Plasmodium falciparum GyrA", PLoS ONE, 10 (11), e0142313 (2015).
  59. Furuse, M., Tamogami, J., Hosaka, T., Kikukawa, T., Shinya, N., Hato, M., Ohsawa, N., Kim, S. Y., Jung, KH., Demura, M., Miyauchi, S., Kamo, N., Shimono, K., Kimura-Someya, T., Yokoyama, S., and Shirouzu, M. "Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum", Acta Crystallogr. D Biol. Crystallogr., 71 (11), 2203–2216 (2015).
  60. Tokmakov, A. A., Kurotani, A., Ikeda, M., Terazawa, Y., Shirouzu, M., Stefanov, V., Sakurai, T., and Yokoyama, S. "Content of intrinsic disorder influences the outcome of cell-free protein synthesis", Sci Rep, 5, 14079 (2015).
  61. Yoshida, H., Park, SY., Oda, T., Akiyoshi, T., Sato, M., Shirouzu, M., Tsuda, K., Kuwasako, K., Unzai, S., Muto, Y., Urano, T., and Obayashi, E. "A novel 3' splice site recognition by the two zinc fingers in the U2AF small subunit", Genes Dev., 29 (15), 1649–1660 (2015).
  62. Ohtake, K., Yamaguchi, A., Mukai, T., Kashimura, H., Hirano, N., Haruki, M., Kohashi, S., Yamagishi, K., Murayama, K., Tomabechi, Y., Itagaki, T., Akasaka, R., Kawazoe, M., Takemoto, C., Shirouzu, M., Yokoyama, S., and Sakamoto, K. "Protein stabilization utilizing a redefined codon", Sci Rep, 5, 9762, (2015).
  63. Morikawa, M., Yajima, H., Nitta, R., Inoue, S., Ogura, T., Sato, C., and Hirokawa, N. "X-ray and Cryo-EM structures reveal mutual conformational changes of Kinesin and GTP-state microtubules upon binding", EMBO J., 34 (9), 1270–1286 (2015).
  64. Suzuki, M., Sasabe, J., Miyoshi, Y., Kuwasako, K., Muto, Y., Hamase, K., Matsuoka, M., Imanishi, N., and Aiso, S. "Glycolytic flux controls D-serine synthesis through glyceraldehyde-3-phosphate dehydrogenase in astrocytes", Proc. Natl. Acad. Sci. U.S.A., 112 (17), E2217–2224 (2015).
  65. Tanabe, H., Fujii, Y., Okada-Iwabu, M., Iwabu, M., Nakamura, Y., Hosaka, T., Motoyama, K., Ikeda, M., Wakiyama, M., Terada, T., Ohsawa, N., Hato, M., Ogasawara, S., Hino, T., Murata, T., Iwata, S., Hirata, K., Kawano, Y., Yamamoto, M., Kimura-Someya, T., Shirouzu, M., Yamauchi, T., Kadowaki, T., and Yokoyama, S. "Crystal structures of the human adiponectin receptors", Nature, 520 (7547), 312–316 (2015).
  66. Tochio, N., Umehara, T., Nakabayashi, K., Yoneyama, M., Tsuda, K., Shirouzu, M., Koshiba, S., Watanabe, S., Kigawa, T., Sasazuki, T., Shirasawa, S., and Yokoyama, S. "Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT", J. Struct. Funct. Genomics, 16 (2), 55–65 (2015).
  67. Terasawa, K., Rajapakshe, A. R., Podyma-Inoue, K. A., Mishima-Tsumagari, C., Yanagishita, M., and Hara-Yokoyama, M. "Preferential recognition of isocitrate dehydrogenase by a rabbit monoclonal antibody (ab124797) against the C-terminal peptide of RANKL", J. Immunol. Methods, 420, 1–10 (2015).
  68. Tanabe, H., Motoyama, K., Ikeda, M., Wakiyama, M., Terada, T., Ohsawa, N., Hosaka, T., Hato, M., Fujii, Y., Nakamura, Y., Ogasawara, S., Hino, T., Murata, T., Iwata, S., Okada-Iwabu, M., Iwabu, M., Hirata, K., Kawano, Y., Yamamoto, M., Kimura-Someya, T., Shirouzu, M., Yamauchi, T., Kadowaki, T., and Yokoyama, S. "Expression, purification, crystallization, and preliminary X-ray crystallographic studies of the human adiponectin receptors, AdipoR1 and AdipoR2", J. Struct. Funct. Genomics, 16 (1), 11–23 (2015).
  69. Kanamori, T., Ohzeki, H., Masaki, Y., Ohkubo, A., Takahashi, M., Tsuda, K., Ito, T., Shirouzu, M., Kuwasako, K., Muto, Y., Sekine, M., and Seio, K. "Controlling the fluorescence of benzofuran-modified uracil residues in oligonucleotides by triple-helix formation", Chembiochem, 16 (1), 167–176 (2014).
  70. Nishii, W., Kukimoto-Niino, M., Terada, T., Shirouzu, M., Muramatsu, T., Kojima, M., Kihara, H., and Yokoyama, S. "A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis", Nat. Chem. Biol., 11 (1), 46–51 (2014).
  71. Balogun, E. O., Inaoka, D. K., Shiba, T., Kido, Y., Tsuge, C., Nara, T., Aoki, T., Honma, T., Tanaka, A., Inoue, M., Matsuoka, S., Michels, P. A., Kita, K., and Harada, S. "Molecular basis for the reverse reaction of African human trypanosomes glycerol kinase", Mol. Microbiol., 94 (6), 1315–1329 (2014).
  72. Tsuda, K., Kuwasako, K., Nagata, T., Takahashi, M., Kigawa, T., Kobayashi, N., Güntert, P., Shirouzu, M., Yokoyama, S., and Muto, Y. "Novel RNA recognition motif domain in the cytoplasmic polyadenylation element binding protein 3", Proteins, 82 (10), 2879–2886 (2014).
  73. Kobayashi, T., Shimabukuro-Demoto, S., Yoshida-Sugitani, R., Furuyama-Tanaka, K., Karyu, H., Sugiura, Y., Shimizu, Y., Hosaka, T., Goto, M., Kato, N., Okamura, T., Suematsu, M., Yokoyama, S., and Toyama-Sorimachi, N. "The histidine transporter SLC15A4 coordinates mTOR-dependent inflammatory responses and pathogenic antibody production", Immunity, 41 (3), 375–388 (2014).
  74. Kuwasako, K., Takahashi, M., Unzai, S., Tsuda, K., Yoshikawa, S., He, F., Kobayashi, N., Güntert, P., Shirouzu, M., Ito, T., Tanaka, A., Yokoyama, S., Hagiwara, M., Kuroyanagi, H., and Muto, Y. "RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing", Nat. Struct. Mol. Biol., 21 (9), 778–786 (2014).
  75. Bin, BH., Hojyo, S., Hosaka, T., Bhin, J., Kano, H., Miyai, T., Ikeda, M., Kimura-Someya, T., Shirouzu, M., Cho, EG., Fukue, K., Kambe, T., Ohashi, W., Kim, KH., Seo, J., Choi, DH., Nam, YJ., Hwang, D., Fukunaka, A., Fujitani, Y., Yokoyama, S., Superti-Furga, A., Ikegawa, S., Lee, T. R., and Fukada, T. "Molecular pathogenesis of Spondylocheirodysplastic Ehlers-Danlos syndrome caused by mutant ZIP13 proteins", EMBO Mol Med, 6 (8), 1028–1042 (2014).
  76. Niwa, H., Mikuni, J., Sasaki, S., Tomabechi, Y., Honda, K., Ikeda, M., Ohsawa, N., Wakiyama, M., Handa, N., Shirouzu, M., Honma, T., Tanaka, A., and Yokoyama, S. "Crystal structures of the S6K1 kinase domain in complexes with inhibitors", J. Struct. Funct. Genomics, 15 (3), 153–164 (2014).
  77. Yanagisawa, T., Takahashi, M., Mukai, T., Sato, S., Wakamori, M., Shirouzu, M., Sakamoto, K., Umehara, T., and Yokoyama, S. "Multiple site-specific installations of Nε-monomethyl-L-lysine into histone proteins by cell-based and cell-free protein synthesis", Chembiochem, 15 (12), 1830–1838 (2014).
  78. Hato, M., Hosaka, T., Tanabe, H., Kitsunai, T., and Yokoyama, S. "A new manual dispensing system for in meso membrane protein crystallization with using a stepping motor-based dispenser", J. Struct. Funct. Genomics, 15 (3), 165–171 (2014).
  79. Kusano, S., Kukimoto-Niino, M., Satta, Y., Ohsawa, N., Uchikubo-Kamo, T., Wakiyama, M., Ikeda, M., Terada, T., Yamamoto, K., Nishimura, Y., Shirouzu, M., Sasazuki, T., and Yokoyama, S. "Structural basis for the specific recognition of the major antigenic peptide from the Japanese cedar pollen allergen Cry j 1 by HLA-DP5", J. Mol. Biol., 426 (17), 3016–3027 (2014).
  80. Takeo, K., Tanimura, S., Shinoda, T., Osawa, S., Zahariev, I. k., Takegami, N., Ishizuka-Katsura, Y., Shinya, N., Takagi-Niidome, S., Tominaga, A., Ohsawa, N., Kimura-Someya, T., Shirouzu, M., Yokoshima, S., Yokoyama, S., Fukuyama, T., Tomita, T., and Iwatsubo, T. "Allosteric regulation of γ-secretase activity by a phenylimidazole-type γ-secretase modulator", Proc. Natl. Acad. Sci. U.S.A., 111 (29), 10544–10549 (2014).
  81. Shoji, S., Muto, Y., Ikeda, M., He, F., Tsuda, K., Ohsawa, N., Akasaka, R., Terada, T., Wakiyama, M., Shirouzu, M., and Yokoyama, S. "The zinc-binding region (ZBR) fragment of Emi2 can inhibit APC/C by targeting its association with the coactivator Cdc20 and UBE2C-mediated ubiquitylation", FEBS Open Bio, 4 (1), 689–703 (2014).
  82. Kuratani, M., Yanagisawa, T., Ishii, R., Matsuno, M., Si, SY., Katsura, K., Ushikoshi-Nakayama, R., Shibata, R., Shirouzu, M., Bessho, Y., and Yokoyama, S. "Crystal structure of tRNA m1A58 methyltransferase TrmI from Aquifex aeolicus in complex with S-adenosyl-L-methionine", J. Struct. Funct. Genomics, 15 (3), 173–180 (2014).
  83. Iba, Y., Fujii, Y., Ohshima, N., Sumida, T., Kubota-Koketsu, R., Ikeda, M., Wakiyama, M., Shirouzu, M., Okada, J., Okuno, Y., Kurosawa, Y., and Yokoyama, S. "Conserved neutralizing epitope at globular head of hemagglutinin in H3N2 influenza viruses", J. Virol., 88 (13), 7130–7144 (2014).
  84. Tagami, S., Sekine, SI., Minakhin, L., Esyunina, D., Akasaka, R., Shirouzu, M., Kulbachinskiy, A., Severinov, K., and Yokoyama, S. "Structural basis for promoter specificity switching of RNA polymerase by a phage factor", Genes Dev., 28 (5), 521–531 (2014).
  85. Parker, L. J., Taruya, S., Tsuganezawa, K., Ogawa, N., Mikuni, J., Honda, K., Tomabechi, Y., Handa, N., Shirouzu, M., Yokoyama, S., and Tanaka, A. "Kinase crystal identification and ATP-competitive inhibitor screening using the fluorescent ligand SKF86002", Acta Crystallogr. D Biol. Crystallogr., 70 (2), 392–404 (2014).
  86. Alam, J., Yamato, I., Arai, S., Saijo, S., Mizutani, K., Ishizuka-Katsura, Y., Ohsawa, N., Terada, T., Shirouzu, M., Yokoyama, S., Iwata, S., Kakinuma, Y., and Murata, T. "Mutant LV476-7AA of A-subunit of Enterococcus hirae V1-ATPase: High affinity of A3B3 complex to DF axis and low ATPase activity", Springerplus, 2, 689 (2013).
  87. Sakata, K., Hara, M., Terada, T., Watanabe, N., Takaya, D., Yaguchi, SI., Matsumoto, T., Matsuura, T., Shirouzu, M., Yokoyama, S., Yamaguchi, T., Miyazawa, K., Aizaki, H., Suzuki, T., Wakita, T., Imoto, M., and Kojima, S. "HCV NS3 protease enhances liver fibrosis via binding to and activating TGF-β type I receptor", Sci Rep, 3, 3243 (2013).
  88. Okada-Iwabu, M., Yamauchi, T., Iwabu, M., Honma, T., Hamagami, KI., Matsuda, K., Yamaguchi, M., Tanabe, H., Kimura-Someya, T., Shirouzu, M., Ogata, H., Tokuyama, K., Ueki, K., Nagano, T., Tanaka, A., Yokoyama, S., and Kadowaki, T. "A small-molecule AdipoR agonist for type 2 diabetes and short life in obesity", Nature, 503 (7477), 493–499 (2013).
  89. Minagawa, Y., Ueno, H., Hara, M., Ishizuka-Katsura, Y., Ohsawa, N., Terada, T., Shirouzu, M., Yokoyama, S., Yamato, I., Muneyuki, E., Noji, H., Murata, T., and Iino, R. "Basic properties of rotary dynamics of the molecular motor Enterococcus hirae V1-ATPase", J. Biol. Chem., 288 (45), 32700–32707 (2013).
  90. Alam, M. J., Arai, S., Saijo, S., Suzuki, K., Mizutani, K., Ishizuka-Katsura, Y., Ohsawa, N., Terada, T., Shirouzu, M., Yokoyama, S., Iwata, S., Kakinuma, Y., Yamato, I., and Murata, T. "Loose binding of the DF axis with the A3B3 complex stimulates the initial activity of Enterococcus hirae V1-ATPase", PLoS ONE, 8 (9), e74291 (2013).
  91. Nishikimi, A., Kukimoto-Niino, M., Yokoyama, S., and Fukui, Y. "Immune regulatory functions of DOCK family proteins in health and disease", Exp. Cell Res., 319 (15), 2343–2349 (2013).
  92. Kusano, S. and Yokoyama, S., "Ectodomain structures of the CGRP and AM receptors", Curr. Protein Pept. Sci., 14 (5), 375–385 (2013).
  93. Tsuganezawa, K., Shinohara, Y., Ogawa, N., Tsuboi, S., Okada, N., Mori, M., Yokoyama, S., Noda, N. N., Inagaki, F., Ohsumi, Y., and Tanaka, A. "Two-colored fluorescence correlation spectroscopy screening for LC3-P62 interaction inhibitors", J Biomol Screen, 18 (9), 1103–1109 (2013).
  94. Won, EY., Xie, Y., Takemoto, C., Chen, L., Liu, ZJ., Wang, BC., Lee, D., Woo, EJ., Park, SG., Shirouzu, M., Yokoyama, S., Kim, S. J., and Chi, SW. "High-resolution crystal structure of the catalytic domain of human dual-specificity phosphatase 26", Acta Crystallogr. D Biol. Crystallogr., 69 (6), 1160–1170 (2013).
  95. Balogun, E. O., Inaoka, D. K., Shiba, T., Kido, Y., Nara, T., Aoki, T., Honma, T., Tanaka, A., Inoue, M., Matsuoka, S., Michels, P. AM., Harada, S., and Kita, K. "Biochemical characterization of highly active Trypanosoma brucei gambiense glycerol kinase, a promising drug target", J. Biochem., 154 (1), 77–84 (2013).
  96. Mori, S., Tezuka, Y., Arakawa, A., Handa, N., Shirouzu, M., Akiyama, T., and Yokoyama, S. "Crystal structure of the guanylate kinase domain from discs large homolog 1 (DLG1/SAP97)", Biochem. Biophys. Res. Commun., 435 (3), 334–338 (2013).
  97. Saito, Y., Yuki, H., Kuratani, M., Hashizume, Y., Takagi, S., Honma, T., Tanaka, A., Shirouzu, M., Mikuni, J., Handa, N., Ogahara, I., Sone, A., Najima, Y., Tomabechi, Y., Wakiyama, M., Uchida, N., Tomizawa-Murasawa, M., Kaneko, A., Tanaka, S., Suzuki, N., Kajita, H., Aoki, Y., Ohara, O., Shultz, L. D., Fukami, T., Goto, T., Taniguchi, S., Yokoyama, S., and Ishikawa, F. "A pyrrolo-pyrimidine derivative targets human primary AML stem cells in vivo", Sci Transl Med, 5 (181), 181ra52_1–181ra52_15 (2013).
  98. Nakagawa, H., Kuratani, M., Goto-Ito, S., Ito, T., Katsura, K., Terada, T., Shirouzu, M., Sekine, SI., Shigi, N., and Yokoyama, S. "Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA", Proteins, 81 (7), 1232–1244 (2013).
  99. Shodai, A., Morimura, T., Ido, A., Uchida, T., Ayaki, T., Takahashi, R., Kitazawa, S., Suzuki, S., Shirouzu, M., Kigawa, T., Muto, Y., Yokoyama, S., Takahashi, R., Kitahara, R., Ito, H., Fujiwara, N., and Urushitani, M. "Aberrant assembly of RNA recognition motif 1 links to pathogenic conversion of TAR DNA-binding protein of 43 kDa (TDP-43)", J. Biol. Chem., 288 (21), 14886–14905 (2013).
  100. Padmanabhan, B., Nakamura, Y., Antonyuk, S. V., Strange, R. W., Hasnain, S. S., Yokoyama, S., and Bessho, Y. "Structure of the hypothetical DUF1811-family protein GK0453 from Geobacillus kaustophilus HTA426", Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 69 (4), 342–345 (2013).
  101. Muramatsu, T., Kim, YT., Nishii, W., Terada, T., Shirouzu, M., and Yokoyama, S. "Autoprocessing mechanism of severe acute respiratory syndrome coronavirus 3C-Like protease (SARS-CoV 3CLpro) from its polyproteins", FEBS J., 280 (9), 2002–2013 (2013).
  102. Niwa, H., Handa, N., Tomabechi, Y., Honda, K., Toyama, M., Ohsawa, N., Shirouzu, M., Kagechika, H., Hirano, T., Umehara, T., and Yokoyama, S. "Structures of histone methyltransferase SET7/9 in complexes with adenosylmethionine derivatives", Acta Crystallogr. D Biol. Crystallogr., 69 (4), 595–602 (2013).
  103. Shiba, T., Kido, Y., Sakamoto, K., Inaoka, D. K., Tsuge, C., Tatsumi, R., Takahashi, G., Balogun, E. O., Nara, T., Aoki, T., Honma, T., Tanaka, A., Inoue, M., Matsuoka, S., Saimoto, H., Moore, A. L., Harada, S., and Kita, K. "Structure of the trypanosome cyanide-insensitive alternative oxidase", Proc. Natl. Acad. Sci. U.S.A., 110 (12), 4580–4585 (2013).
  104. Matsumoto, A., Shimizu, Y., Takemoto, C., Ueda, T., Uchiumi, T., and Ito, K. "Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Thermus thermophilus HB8", Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 69 (3), 332–335 (2013).
  105. Takaya, D., Sato, T., Yuki, H., Sasaki, S., Tanaka, A., Yokoyama, S., and Honma, T. "Prediction of ligand-induced structural polymorphism of receptor interaction sites using Machine Learning", J Chem Inf Model, 53 (3), 704–716 (2013).
  106. Rahman, S., Yamato, I., Saijo, S., Mizutani, K., Ishizuka-Katsura, Y., Ohsawa, N., Terada, T., Shirouzu, M., Yokoyama, S., Iwata, S., and Murata, T. "Biochemical and biophysical properties of interactions between subunits of the peripheral stalk region of Human V-ATPase", PLoS ONE, 8 (2), e55704 (2013).
  107. Arai, S., Saijo, S., Suzuki, K., Mizutani, K., Kakinuma, Y., Ishizuka-Katsura, Y., Ohsawa, N., Terada, T., Shirouzu, M., Yokoyama, S., Iwata, S., Yamato, I., and Murata, T. "Rotation mechanism of Enterococcus hirae V1-ATPase based on asymmetric crystal structures", Nature, 493 (7434), 703–707 (2013).
  108. Nagata, T., Tsuda, K., Kobayashi, N., Güntert, P., Yokoyama, S., and Muto, Y. "1H, 13C, and 15N resonance assignments of the dsRBDs of mouse RNA helicase A", Biomol NMR Assign, 7 (1), 69–72 (2012).
  109. Yoshikawa, S., Kukimoto-Niino, M., Parker, L., Handa, N., Terada, T., Fujimoto, T., Terazawa, Y., Wakiyama, M., Sato, M., Sano, S., Kobayashi, T., Tanaka, T., Chen, L., Liu, ZJ., Wang, BC., Shirouzu, M., Kawa, S., Semba, K., Yamamoto, T., and Yokoyama, S. "Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor", Oncogene, 32 (1), 27–38 (2012).